How to copy mesh to new files with Python?
Found how to do it. The code I had was half the solution.

After creating a new file, executing the following script adds the mesh to a collection in the scene as I needed. It assumes there's no collection and only one data block in the blend file.

add_object.py

import bpy

collection = bpy.data.collections.new("Collection 1")
bpy.context.scene.collection.children.link(collection)
collection.objects.link(bpy.data.objects[0])
bpy.ops.wm.save_as_mainfile(filepath=bpy.data.filepath)



To execute the script, I executed this in a loop:

blender.exe  &lt;path_to_new_blend_file&gt; --background --python add_object.py